Re: GSOC [Continuous Integration for all biological applications inside Debian]
[I guess you responded in the wrong thread - but it is nice to know anyway.]
On Fri, Apr 08, 2016 at 03:34:03AM +0200, Steffen Möller wrote:
> Hello,
>
> I have identified (some of the glitches) of the autodock tools and I
> know upstream to already have worked on it, seriously. This is the pack
> and grid on the same frame and incompatibility with the numeric library.
> I'll send them a ping.
>
> Best,
>
> Steffen
>
> On 07/04/16 23:58, Canberk Koç wrote:
> > Hello Andreas,
> >
> > Thanks for rapid response again i talk with my friend he will send an
> > introduction email to list. In test issue i'm confused about something
> > if i delete dh_make section and run adt-run package do automatic test
> > in built time and give no erors i notice that now but can't figure it
> > out why already and working on it. Also i make set -e in unit test
> > file but that fatal eror strings wont exit and work through the end it
> > is another abnormality i found so i want to give you a little update
> > about it.
> > And CC issue i do it right now i think :-)
> >
> > Best Regards
> >
> > Canberk
> >
> > 2016-04-07 9:32 GMT+03:00 Andreas Tille <andreas@an3as.eu
> > <mailto:andreas@an3as.eu>>:
> >
> > Hi Canberk,
> >
> > On Thu, Apr 07, 2016 at 04:42:56AM +0300, Canberk Koç wrote:
> > > >[I think I gave a warning that non-private messages will be
> > answered on
> > > >the mailing list and I hereby doing so shamelessly violating
> > netiquette.
> > > >It would be great if you would answer on list as well.]
> > >
> > > Sorry for miss clicking i forget to reply all.
> >
> > No problem. BTW, the mailing list policy for Debian list is to not CC
> > the original poster but just send to the mailing list. The mail
> > client
> > mutt supports "list-reply" (L) to do this efficiently. I have no idea
> > about other mail clients and whether these might support this. Just
> > telling you that if you might write on other Debian lists people might
> > send angry replies for personal CCs. :-)
> >
> > > I committed the changes to exonerate package i hope i do it right.
> >
> > Yes. You did. :-) I turned your "NMU" into a "Team upload". The
> > test
> > suite can implemented in this way. However, when I actually run the
> > test I get:
> >
> > ...
> > /tmp/exonerate-test.nhNsuB/util/fastasplit.test.sh
> > <http://fastasplit.test.sh>
> > Split fastasplit.test.fasta OK
> > Split into two files as expected
> > Input len 2136
> > Output len 2136
> > Input and output lengths match
> >
> > /tmp/exonerate-test.nhNsuB/util/fastadiff.test.sh
> > <http://fastadiff.test.sh>
> > fastadiff: id mismatch: CALM_HUMAN P53_HUMAN
> > Different seqs recognised as different
> > Identity test OK
> >
> > /tmp/exonerate-test.nhNsuB/util/fastasubseq.test.sh
> > <http://fastasubseq.test.sh>
> > Generated correct subseq
> >
> > /tmp/exonerate-test.nhNsuB/util/fastavalidcds.test.sh
> > <http://fastavalidcds.test.sh>
> >
> > ** (process:7647): WARNING **: odd_length length (7) not divisible
> > by 3
> >
> > ** (process:7647): WARNING **: too_short length (4) not divisible by 3
> >
> > ** (process:7647): WARNING **: no_start missing start codon (has:AAA)
> >
> > ** (process:7647): WARNING **: no_end missing stop codon (has:TTT)
> >
> > ** (process:7647): WARNING **: in_frame_stop contains in-frame
> > stop codon (pos:9, codon:TAG)
> >
> > ** (process:7647): WARNING **: non_acgt_base contains non-ACGT
> > base: [pos: 5 base: N]
> > Validiated CDS sequences OK
> > >valid_seq
> > ATGAAACCCGGGTTTTAA
> > Validated correctly a single seq from input
> >
> > /tmp/exonerate-test.nhNsuB/util/fastaindex.fastafetch.test.sh
> > <http://fastaindex.fastafetch.test.sh>
> > Made index fastafetch.test.idx
> > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> > CALM_HUMAN
> > expect 0
> > >CALM_HUMAN
> > MADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFL
> > TMMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYE
> > EFVQMMTAK
> > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> > P53_HUMAN
> > expect 0
> > >P53_HUMAN
> > MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAA
> > PPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMFCQLAKT
> > CPVQLWVDSTPPPGTRVRAMAIYKQSQHMTEVVRRCPHHERCSDSDGLAPPQHLIRVEGNLRVEYLDDRN
> > TFRHSVVVPYEPPEVGSDCTTIHYNYMCNSSCMGGMNRRPILTIITLEDSSGNLLGRNSFEVHVCACPGR
> > DRRTEEENLRKKGEPHHELPPGSTKRALPNNTSSSPQPKKKPLDGEYFTLQIRGRERFEMFRELNEALEL
> > KDAQAGKEPGGSRAHSSHLKSKKGQSTSRHKKLMFKTEGPDSD
> > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> > A_MISSING_FROM_START
> > expect 1
> > ** FATAL ERROR **: Could not find identifier
> > [A_MISSING_FROM_START] (missing -F ?)
> > exiting ...
> > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> > M_MISSING_FROM_MIDDLE
> > expect 1
> > ** FATAL ERROR **: Could not find identifier
> > [M_MISSING_FROM_MIDDLE] (missing -F ?)
> > exiting ...
> > /usr/bin/fastafetch fastafetch.test.fasta fastafetch.test.idx
> > z_MISSING_FROM_END
> > expect 1
> > ** FATAL ERROR **: Could not find identifier [z_MISSING_FROM_END]
> > (missing -F ?)
> > exiting ...
> > fastaindex fastafetch test OK
> >
> > /tmp/exonerate-test.nhNsuB/util/fastaremove.test.sh
> > <http://fastaremove.test.sh>
> > Have calmodulin in input
> > ** FATAL ERROR **: Could not open list for removal [CALM_HUMAN]
> > exiting ...
> > Calmodulin successfully removed
> > PASS
> >
> >
> > These "FATAL ERROR" strings in connection with "PASS" do not sound
> > convincing. I wonder whether the build time tests are different
> > in this aspect.
> >
> >
> > > In MoM issue i want to do it but my mid-term exams start and
> > they'll finish
> > > 25 April i can do it after that date. And i want to ask you one
> > friend of
> > > mine wants to work it on too can we work together in that project.
> >
> > We'd be happy about any volunteer contributing to the Debian Med
> > project.
> >
> > Kind regards
> >
> > Andreas.
> >
> > --
> > http://fam-tille.de
> >
> >
> >
> >
> > --
> >
> > --
> >
> > Canberk Koç
> > https://about.me/canberkkoc
> >
> > <https://about.me/canberkkoc?promo=email_sig&utm_source=email_sig&utm_medium=email_sig&utm_campaign=external_links>
> >
>
>
--
http://fam-tille.de
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